Study design: Three-arm, parallel, randomized, placebo-controlled, assessor-blinded trial. Objective: To compare the immediate effect of manual therapy at the upper thoracic spine on the cardiovascular autonomic control of patients with musculoskeletal pain. Summary of background data: Musculoskeletal pain increases the risk of cardiovascular events. Thus, manual therapy applied to the upper thoracic region is likely efficient to improve the cardiac autonomic control. Methods: The study included 59 patients with musculoskeletal pain enrolled at an outpatient clinic. Participants were randomly assigned to spinal manipulation (n = 19), myofascial manipulation (n = 20), or placebo (n = 20) administered to the upper thoracic region. Resting heart rate variability provided indexes of the cardiac autonomic control, and the blood pressure response to the cold pressor test as a proxy of the sympathetic responsiveness to a stressor stimulus. Results: Groups were similar for baseline variables except for blood pressure. Two-way repeated-measures one-way analysis of covariance (ANCOVA) revealed that only spinal manipulation induced immediate increase of the square root of the mean squared differences of successive RR intervals (RMSSD), absolute (ms2), and normalized units (n.u.) of the high-frequency power (HF) as compared with pre-intervention evaluation, indicating an improvement in the parasympathetic activity to the heart. Normalized units of low-frequency power (LF) and the LF/HF ratio reduced after the spinal manipulation solely, suggesting a reduction of the sympathetic activity to the heart. There were no significant differences in the blood pressure responsiveness among the three treatments. There were no adverse events. Conclusion: In patients with musculoskeletal pain, spinal manipulation on the upper thoracic spine led to an immediate improvement in the resting cardiac autonomic control without an effect on the blood pressure responsiveness to a sympathoexcitatory stimulus. Myofascial manipulation or placebo did not change cardiovascular autonomic control.Level of Evidence: 2.